The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
metaxa 2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data
Abstract
The ribosomal rRNA genes are widely used as genetic markers for taxonomic identification of microbes. Particularly the small subunit (SSU; 16S/18S) rRNA gene is frequently used for species‐ or genus‐level identification, but also the large subunit (LSU; 23S/28S) rRNA gene is employed in taxonomic assignment. The metaxa software tool is a popular utility for extracting partial rRNA sequences from large sequencing data sets and assigning them to an archaeal, bacterial, nuclear eukaryote, mitochondrial or chloroplast origin. This study describes a comprehensive update to metaxa – metaxa 2 – that extends the capabilities of the tool, introducing support for the LSU rRNA gene, a greatly improved classifier allowing classification down to genus or species level, as well as enhanced support for short‐read (100 bp) and paired‐end sequences, among other changes. The performance of metaxa 2 was compared to other commonly used taxonomic classifiers, showing that metaxa 2 often outperforms previous methods in terms of making correct predictions while maintaining a low misclassification rate. metaxa 2 is freely available from http://microbiology.se/software/metaxa2/.
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QIIME allows analysis of high-throughput community sequencing data
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The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
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Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
DeSantis, T. Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E. L., Keller, K., Huber, T., Dalevi, D., Hu, P., & Andersen, G. L. (2006) · Applied and Environmental Microbiology · doi:10.1128/aem.03006-05 · Cited by 10,891
Accelerated Profile HMM Searches
Eddy, S. R. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002195 · Cited by 6,975
Towards next-generation biodiversity assessment using DNA metabarcoding
TABERLET, P., COISSAC, E., POMPANON, F., BROCHMANN, C., & WILLERSLEV, E. (2012) · Molecular Ecology · doi:10.1111/j.1365-294x.2012.05470.x · Cited by 1,907
Cited by
Pärnänen, K., Karkman, A., Hultman, J., Lyra, C., Bengtsson-Palme, J., Larsson, D. G. J., Rautava, S., Isolauri, E., Salminen, S., Kumar, H., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-06393-w · Cited by 678
Self-citationAccuracy of taxonomy prediction for 16S rRNA and fungal ITS sequences
Edgar, R. C. (2018) · PeerJ · doi:10.7717/peerj.4652 · Cited by 319
Svartström, O., Alneberg, J., Terrapon, N., Lombard, V., de Bruijn, I., Malmsten, J., Dalin, A.-M., EL Muller, E., Shah, P., Wilmes, P., et al. (2017) · The ISME Journal · doi:10.1038/ismej.2017.108 · Cited by 161
Reservoirs of antimicrobial resistance genes in retail raw milk
Liu, J., Zhu, Y., Jay-Russell, M., Lemay, D. G., & Mills, D. A. (2020) · Microbiome · doi:10.1186/s40168-020-00861-6 · Cited by 99
Pärnänen, K. M., Hultman, J., Markkanen, M., Satokari, R., Rautava, S., Lamendella, R., Wright, J., McLimans, C. J., Kelleher, S. L., & Virta, M. P. (2022) · The American Journal of Clinical Nutrition · doi:10.1093/ajcn/nqab353 · Cited by 99
Metadata
- Authors
- Bengtsson‐Palme, J., Hartmann, M., Eriksson, K. M., Pal, C., Thorell, K., Larsson, D. G. J., & Nilsson, R. H.
- Venue
- Molecular Ecology Resources
- Publisher
- Wiley
- Published
- 2015-03-23
- Volume
- 15
- Issue
- 6
- Pages
- 1403-1414
- ISSN
- 1755-098X (ISSN-L)
- 1755-0998
- OpenAlex
- W2137107630
- Cited by
- 459
- References
- 5
- FWCI
- 12.35
- Type
- journal article
- Language
- en
- Open access
- closed
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- Bengtsson‐Palme, J., Hartmann, M., Eriksson, K. M., Pal, C., Thorell, K., Larsson, D. G. J., & Nilsson, R. H. (2015). metaxa 2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data. Molecular Ecology Resources. https://doi.org/10.1111/1755-0998.12399
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